Zhang Xiaohua Douglas, Heyse Joseph F
Biometrics Research and BARDS, Merck Research Laboratories, West Point, PA 19486, USA.
Bioinformatics. 2009 Apr 1;25(7):841-4. doi: 10.1093/bioinformatics/btp082. Epub 2009 Feb 17.
For genome-scale RNAi research, it is critical to investigate sample size required for the achievement of reasonably low false negative rate (FNR) and false positive rate.
The analysis in this article reveals that current design of sample size contributes to the occurrence of low signal-to-noise ratio in genome-scale RNAi projects. The analysis suggests that (i) an arrangement of 16 wells per plate is acceptable and an arrangement of 20-24 wells per plate is preferable for a negative control to be used for hit selection in a primary screen without replicates; (ii) in a confirmatory screen or a primary screen with replicates, a sample size of 3 is not large enough, and there is a large reduction in FNRs when sample size increases from 3 to 4. To search a tradeoff between benefit and cost, any sample size between 4 and 11 is a reasonable choice. If the main focus is the selection of siRNAs with strong effects, a sample size of 4 or 5 is a good choice. If we want to have enough power to detect siRNAs with moderate effects, sample size needs to be 8, 9, 10 or 11. These discoveries about sample size bring insight to the design of a genome-scale RNAi screen experiment.
对于全基因组规模的RNA干扰研究而言，探究实现合理低假阴性率（FNR）和假阳性率所需的样本量至关重要。
本文的分析表明，当前样本量的设计导致了全基因组规模RNA干扰项目中低信噪比情况的出现。该分析表明：（i）对于无重复的初次筛选中用于命中选择的阴性对照，每板16孔的布局是可以接受的，每板20 - 24孔的布局则更为可取；（ii）在验证性筛选或有重复的初次筛选中，样本量为3不够大，当样本量从3增加到4时，假阴性率会大幅降低。为了在效益和成本之间寻求平衡，4到11之间的任何样本量都是合理的选择。如果主要关注的是具有强效的小干扰RNA（siRNA）的选择，样本量为4或5是个不错的选择。如果我们希望有足够的能力检测具有中等效果的siRNA，样本量需要为8、9、10或11。这些关于样本量的发现为全基因组规模RNA干扰筛选实验的设计提供了见解。
